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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.13 (e19d516)

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2024-05-26, 16:58 CEST based on data in: /storage/qc_camda/work_dir/short_read_qc/4_summary/fastqc_post


        General Statistics

        Showing 248/248 rows and 4/5 columns.
        Sample Name% Dups% GCRead LengthM Seqs
        BER_0XMTAHIFY_1
        29.3%
        56%
        144 bp
        33.8
        BER_0XMTAHIFY_2
        28.8%
        56%
        144 bp
        33.8
        BER_1FZ1M3LBT_1
        7.8%
        53%
        137 bp
        0.7
        BER_1FZ1M3LBT_2
        7.6%
        53%
        137 bp
        0.7
        BER_5UIO53M4H_1
        10.8%
        47%
        143 bp
        25.9
        BER_5UIO53M4H_2
        10.7%
        47%
        143 bp
        25.9
        BER_62VRQ43DO_1
        5.6%
        46%
        143 bp
        1.8
        BER_62VRQ43DO_2
        5.4%
        46%
        143 bp
        1.8
        BER_6LAJ3M790_1
        4.4%
        53%
        143 bp
        1.7
        BER_6LAJ3M790_2
        4.3%
        53%
        143 bp
        1.7
        BER_95LGP511C_1
        4.2%
        51%
        144 bp
        2.2
        BER_95LGP511C_2
        4.1%
        51%
        144 bp
        2.2
        BER_AB4OX8WDL_1
        10.4%
        52%
        143 bp
        22.0
        BER_AB4OX8WDL_2
        10.2%
        52%
        143 bp
        22.0
        BER_DQQNEILON_1
        6.8%
        50%
        142 bp
        0.7
        BER_DQQNEILON_2
        6.7%
        50%
        142 bp
        0.7
        BER_GDW7R8G7U_1
        9.1%
        50%
        132 bp
        0.6
        BER_GDW7R8G7U_2
        8.9%
        50%
        132 bp
        0.6
        BER_ILKOKA4FY_1
        3.8%
        54%
        143 bp
        3.6
        BER_ILKOKA4FY_2
        3.7%
        54%
        143 bp
        3.6
        BER_KSGJ4JDMP_1
        13.4%
        49%
        141 bp
        20.7
        BER_KSGJ4JDMP_2
        13.2%
        50%
        141 bp
        20.7
        BER_N4UZTNZWM_1
        12.2%
        45%
        143 bp
        20.6
        BER_N4UZTNZWM_2
        12.1%
        45%
        143 bp
        20.6
        BER_Q18XQVS7O_1
        10.7%
        52%
        141 bp
        32.6
        BER_Q18XQVS7O_2
        10.6%
        52%
        141 bp
        32.6
        BER_U0X73SKMV_1
        4.4%
        53%
        144 bp
        4.4
        BER_U0X73SKMV_2
        4.3%
        53%
        144 bp
        4.4
        BER_ZFYS1K2UB_1
        7.8%
        52%
        136 bp
        1.2
        BER_ZFYS1K2UB_2
        7.6%
        52%
        136 bp
        1.2
        BER_ZQVJSZP1R_1
        5.2%
        50%
        142 bp
        1.8
        BER_ZQVJSZP1R_2
        5.1%
        50%
        142 bp
        1.8
        DOH_UVQTUJ3WY_1
        9.2%
        46%
        137 bp
        1.5
        DOH_UVQTUJ3WY_2
        8.9%
        46%
        137 bp
        1.5
        DOH_Z97N7FJ2K_1
        10.8%
        50%
        136 bp
        2.0
        DOH_Z97N7FJ2K_2
        10.4%
        50%
        136 bp
        2.0
        FAI_3H4A57Q94_1
        56.0%
        50%
        144 bp
        36.0
        FAI_3H4A57Q94_2
        55.8%
        50%
        144 bp
        36.0
        ILR_0QOJ42GKE_1
        29.8%
        52%
        145 bp
        36.9
        ILR_0QOJ42GKE_2
        29.5%
        52%
        145 bp
        36.9
        ILR_1E4I5PCKR_1
        35.7%
        60%
        144 bp
        26.7
        ILR_1E4I5PCKR_2
        35.5%
        60%
        144 bp
        26.7
        ILR_29PLYWCEQ_1
        30.3%
        60%
        147 bp
        30.4
        ILR_29PLYWCEQ_2
        30.1%
        60%
        147 bp
        30.4
        ILR_3ZSVTU0OG_1
        10.3%
        44%
        148 bp
        2.7
        ILR_3ZSVTU0OG_2
        10.2%
        44%
        148 bp
        2.7
        ILR_5O6P46B1O_1
        13.7%
        48%
        145 bp
        24.5
        ILR_5O6P46B1O_2
        13.4%
        48%
        145 bp
        24.5
        ILR_6GO056W16_1
        16.5%
        47%
        144 bp
        20.7
        ILR_6GO056W16_2
        16.4%
        47%
        144 bp
        20.7
        ILR_6YBM27DNP_1
        43.2%
        58%
        147 bp
        59.3
        ILR_6YBM27DNP_2
        42.8%
        58%
        147 bp
        59.3
        ILR_7WU54RPYQ_1
        11.2%
        60%
        148 bp
        3.1
        ILR_7WU54RPYQ_2
        11.0%
        60%
        148 bp
        3.1
        ILR_8DDEILP5T_1
        10.0%
        49%
        145 bp
        34.3
        ILR_8DDEILP5T_2
        9.9%
        49%
        145 bp
        34.3
        ILR_8HCRBXWIW_1
        66.7%
        61%
        147 bp
        32.7
        ILR_8HCRBXWIW_2
        66.2%
        61%
        147 bp
        32.7
        ILR_A1FW6B4A2_1
        43.7%
        59%
        146 bp
        36.3
        ILR_A1FW6B4A2_2
        43.6%
        59%
        146 bp
        36.3
        ILR_BAT5NZLL5_1
        17.3%
        49%
        144 bp
        22.8
        ILR_BAT5NZLL5_2
        17.0%
        49%
        144 bp
        22.8
        ILR_GHWIJHC9P_1
        50.3%
        36%
        142 bp
        44.0
        ILR_GHWIJHC9P_2
        49.2%
        36%
        142 bp
        44.0
        ILR_JB0EYR720_1
        14.1%
        42%
        145 bp
        18.4
        ILR_JB0EYR720_2
        13.9%
        42%
        145 bp
        18.4
        ILR_KSZINB6GM_1
        15.3%
        48%
        145 bp
        44.0
        ILR_KSZINB6GM_2
        15.0%
        48%
        145 bp
        44.0
        ILR_KX055AXB1_1
        6.1%
        49%
        148 bp
        4.2
        ILR_KX055AXB1_2
        6.1%
        49%
        148 bp
        4.2
        ILR_L0BHYTAS7_1
        15.3%
        48%
        144 bp
        39.2
        ILR_L0BHYTAS7_2
        15.0%
        48%
        144 bp
        39.2
        ILR_LYUXMH4S1_1
        52.9%
        62%
        146 bp
        46.9
        ILR_LYUXMH4S1_2
        52.6%
        62%
        146 bp
        46.9
        ILR_MEBWWUJ6Y_1
        15.1%
        45%
        144 bp
        22.5
        ILR_MEBWWUJ6Y_2
        14.7%
        45%
        144 bp
        22.5
        ILR_SRA8DHJ7G_1
        20.4%
        47%
        146 bp
        36.3
        ILR_SRA8DHJ7G_2
        20.4%
        47%
        146 bp
        36.3
        ILR_SS558Z75U_1
        15.7%
        53%
        143 bp
        23.2
        ILR_SS558Z75U_2
        15.3%
        53%
        143 bp
        23.2
        ILR_TUND80BTH_1
        50.1%
        59%
        144 bp
        40.3
        ILR_TUND80BTH_2
        49.9%
        59%
        144 bp
        40.3
        ILR_TX8UOFVBU_1
        35.7%
        56%
        145 bp
        32.5
        ILR_TX8UOFVBU_2
        35.3%
        56%
        145 bp
        32.5
        ILR_U6M78A4O4_1
        22.7%
        53%
        146 bp
        31.7
        ILR_U6M78A4O4_2
        22.4%
        53%
        146 bp
        31.7
        ILR_UOGEDBXYR_1
        16.1%
        55%
        141 bp
        26.7
        ILR_UOGEDBXYR_2
        15.7%
        55%
        141 bp
        26.7
        ILR_VE7RXHRDB_1
        52.6%
        59%
        142 bp
        36.2
        ILR_VE7RXHRDB_2
        52.2%
        59%
        142 bp
        36.2
        ILR_WBTPZ2RH8_1
        54.6%
        53%
        144 bp
        46.1
        ILR_WBTPZ2RH8_2
        53.7%
        53%
        144 bp
        46.1
        ILR_WJ0WL2U4N_1
        18.8%
        51%
        144 bp
        52.3
        ILR_WJ0WL2U4N_2
        18.5%
        51%
        144 bp
        52.3
        ILR_YGMN39LS1_1
        15.2%
        50%
        145 bp
        24.1
        ILR_YGMN39LS1_2
        15.1%
        50%
        145 bp
        24.1
        ILR_ZAOK979DR_1
        44.4%
        59%
        146 bp
        52.4
        ILR_ZAOK979DR_2
        43.9%
        59%
        146 bp
        52.4
        KYI_BLCI47B1L_1
        9.0%
        61%
        138 bp
        1.8
        KYI_BLCI47B1L_2
        8.9%
        61%
        138 bp
        1.8
        KYI_FE49Q5JU5_1
        9.0%
        65%
        137 bp
        3.3
        KYI_FE49Q5JU5_2
        8.7%
        65%
        137 bp
        3.3
        LIS_CGDQAMXOW_1
        7.2%
        51%
        148 bp
        2.2
        LIS_CGDQAMXOW_2
        7.1%
        51%
        148 bp
        2.2
        NYC_0OSAG4JMN_1
        20.0%
        42%
        144 bp
        12.6
        NYC_0OSAG4JMN_2
        20.2%
        42%
        144 bp
        12.6
        NYC_11QGJCLNF_1
        8.1%
        48%
        139 bp
        16.3
        NYC_11QGJCLNF_2
        7.9%
        48%
        139 bp
        16.3
        NYC_16YLK6NTS_1
        6.6%
        46%
        140 bp
        12.1
        NYC_16YLK6NTS_2
        6.5%
        46%
        140 bp
        12.1
        NYC_2D1412PIY_1
        9.9%
        48%
        143 bp
        14.7
        NYC_2D1412PIY_2
        9.8%
        48%
        143 bp
        14.7
        NYC_8EQFI80TE_1
        14.5%
        45%
        143 bp
        16.1
        NYC_8EQFI80TE_2
        14.4%
        45%
        143 bp
        16.1
        NYC_FVV7BKROW_1
        9.8%
        46%
        144 bp
        24.3
        NYC_FVV7BKROW_2
        9.6%
        46%
        144 bp
        24.3
        NYC_JG50JE6NW_1
        11.0%
        49%
        144 bp
        17.9
        NYC_JG50JE6NW_2
        10.9%
        49%
        144 bp
        17.9
        NYC_PHVHF8LRO_1
        7.0%
        47%
        143 bp
        13.3
        NYC_PHVHF8LRO_2
        6.8%
        47%
        143 bp
        13.3
        NYC_QLC9W450U_1
        6.6%
        46%
        143 bp
        16.8
        NYC_QLC9W450U_2
        6.5%
        46%
        143 bp
        16.8
        NYC_V3U3SWRLN_1
        11.0%
        49%
        141 bp
        12.0
        NYC_V3U3SWRLN_2
        11.0%
        49%
        141 bp
        12.0
        Other_00NLH4DKH_1
        5.6%
        60%
        133 bp
        12.4
        Other_00NLH4DKH_2
        5.6%
        60%
        133 bp
        12.4
        Other_0AWFPD6K1_1
        6.2%
        57%
        140 bp
        29.0
        Other_0AWFPD6K1_2
        6.1%
        57%
        140 bp
        29.0
        Other_2MFW9YKGQ_1
        11.1%
        47%
        136 bp
        1.0
        Other_2MFW9YKGQ_2
        11.0%
        47%
        136 bp
        1.0
        Other_34XFCIUBK_1
        5.9%
        47%
        143 bp
        2.4
        Other_34XFCIUBK_2
        5.7%
        46%
        143 bp
        2.4
        Other_3QQCWK2NI_1
        5.5%
        51%
        144 bp
        2.4
        Other_3QQCWK2NI_2
        5.4%
        51%
        144 bp
        2.4
        Other_5BU97OHW4_1
        5.3%
        52%
        145 bp
        2.8
        Other_5BU97OHW4_2
        5.2%
        52%
        145 bp
        2.8
        Other_5PWZ7APWV_1
        6.7%
        55%
        143 bp
        2.4
        Other_5PWZ7APWV_2
        6.6%
        55%
        143 bp
        2.4
        Other_5YVICV67E_1
        7.7%
        44%
        147 bp
        4.0
        Other_5YVICV67E_2
        7.7%
        44%
        147 bp
        4.0
        Other_78KC5QW19_1
        4.9%
        60%
        144 bp
        3.0
        Other_78KC5QW19_2
        4.8%
        60%
        144 bp
        3.0
        Other_8B7NCBIU6_1
        5.9%
        61%
        145 bp
        4.3
        Other_8B7NCBIU6_2
        5.8%
        61%
        145 bp
        4.3
        Other_8BJAQLTL5_1
        8.0%
        58%
        145 bp
        25.8
        Other_8BJAQLTL5_2
        7.9%
        58%
        145 bp
        25.8
        Other_9EEW8UKQ5_1
        11.2%
        53%
        141 bp
        30.6
        Other_9EEW8UKQ5_2
        11.2%
        53%
        141 bp
        30.6
        Other_AFLHRJO9U_1
        76.6%
        55%
        82 bp
        0.8
        Other_AFLHRJO9U_2
        76.4%
        55%
        82 bp
        0.8
        Other_B8T9MC9HX_1
        25.1%
        55%
        126 bp
        0.3
        Other_B8T9MC9HX_2
        24.7%
        54%
        126 bp
        0.3
        Other_BUB0790DM_1
        22.3%
        62%
        136 bp
        2.1
        Other_BUB0790DM_2
        22.1%
        62%
        136 bp
        2.1
        Other_C4I49RDEQ_1
        9.2%
        54%
        145 bp
        17.9
        Other_C4I49RDEQ_2
        9.1%
        54%
        145 bp
        17.9
        Other_CXM0JSR2Z_1
        9.8%
        54%
        144 bp
        18.4
        Other_CXM0JSR2Z_2
        9.7%
        54%
        144 bp
        18.4
        Other_E5BBSE6CJ_1
        5.2%
        57%
        141 bp
        9.5
        Other_E5BBSE6CJ_2
        5.1%
        57%
        141 bp
        9.5
        Other_ERN8QI845_1
        10.1%
        51%
        145 bp
        26.9
        Other_ERN8QI845_2
        10.0%
        51%
        145 bp
        26.9
        Other_FK707F15I_1
        29.3%
        63%
        98 bp
        2.3
        Other_FK707F15I_2
        29.2%
        63%
        98 bp
        2.3
        Other_H6EBVGJ2E_1
        8.6%
        50%
        140 bp
        17.6
        Other_H6EBVGJ2E_2
        8.5%
        50%
        140 bp
        17.6
        Other_L7WYL7CNT_1
        33.3%
        48%
        143 bp
        22.5
        Other_L7WYL7CNT_2
        32.9%
        48%
        143 bp
        22.5
        Other_OJR6I7W48_1
        67.4%
        55%
        93 bp
        0.4
        Other_OJR6I7W48_2
        67.2%
        54%
        93 bp
        0.4
        Other_OKO6BXQLU_1
        18.8%
        63%
        141 bp
        2.0
        Other_OKO6BXQLU_2
        18.6%
        63%
        141 bp
        2.0
        Other_PAPFIWRTK_1
        8.9%
        52%
        140 bp
        2.1
        Other_PAPFIWRTK_2
        8.7%
        52%
        140 bp
        2.1
        Other_Q6XPA2EHD_1
        42.9%
        58%
        146 bp
        44.8
        Other_Q6XPA2EHD_2
        42.4%
        58%
        146 bp
        44.8
        Other_QNPOGJMC5_1
        30.0%
        52%
        139 bp
        21.5
        Other_QNPOGJMC5_2
        28.8%
        52%
        139 bp
        21.5
        Other_RGFMTG8DA_1
        5.2%
        56%
        144 bp
        1.9
        Other_RGFMTG8DA_2
        5.1%
        55%
        144 bp
        1.9
        Other_RGXB25H7Z_1
        12.7%
        53%
        142 bp
        28.0
        Other_RGXB25H7Z_2
        12.5%
        53%
        142 bp
        28.0
        Other_RNRMA0LV4_1
        14.5%
        49%
        142 bp
        20.4
        Other_RNRMA0LV4_2
        14.3%
        49%
        142 bp
        20.4
        Other_RVYJC5DO1_1
        10.2%
        60%
        132 bp
        2.2
        Other_RVYJC5DO1_2
        10.0%
        60%
        132 bp
        2.2
        Other_S7DQERLHT_1
        5.8%
        62%
        145 bp
        3.0
        Other_S7DQERLHT_2
        5.7%
        62%
        145 bp
        3.0
        Other_T6BNL7N55_1
        26.4%
        63%
        132 bp
        1.9
        Other_T6BNL7N55_2
        26.2%
        63%
        132 bp
        1.9
        Other_TT544EJOO_1
        8.3%
        44%
        142 bp
        2.8
        Other_TT544EJOO_2
        8.1%
        44%
        142 bp
        2.8
        Other_UEPCFO8PJ_1
        20.9%
        43%
        141 bp
        1.3
        Other_UEPCFO8PJ_2
        20.7%
        43%
        141 bp
        1.3
        Other_V33D0LP6V_1
        5.8%
        56%
        146 bp
        8.7
        Other_V33D0LP6V_2
        5.8%
        56%
        146 bp
        8.7
        Other_VS30LZK7C_1
        7.0%
        56%
        144 bp
        5.2
        Other_VS30LZK7C_2
        6.9%
        56%
        144 bp
        5.2
        Other_W8SZWP7KP_1
        8.2%
        51%
        142 bp
        1.3
        Other_W8SZWP7KP_2
        8.0%
        51%
        142 bp
        1.3
        Other_WTSQ2F9Z4_1
        11.5%
        55%
        144 bp
        33.6
        Other_WTSQ2F9Z4_2
        11.2%
        55%
        144 bp
        33.6
        Other_XC0RXUORH_1
        6.2%
        55%
        147 bp
        5.2
        Other_XC0RXUORH_2
        6.1%
        55%
        147 bp
        5.2
        Other_XG8YAUERB_1
        19.5%
        49%
        147 bp
        5.2
        Other_XG8YAUERB_2
        19.5%
        49%
        147 bp
        5.2
        Other_XYFIINCYN_1
        10.1%
        61%
        146 bp
        8.2
        Other_XYFIINCYN_2
        9.9%
        61%
        146 bp
        8.2
        Other_Y6VP0ITGO_1
        5.7%
        56%
        144 bp
        2.3
        Other_Y6VP0ITGO_2
        5.6%
        56%
        144 bp
        2.3
        Other_YMPELJW2W_1
        11.5%
        61%
        148 bp
        3.9
        Other_YMPELJW2W_2
        11.5%
        61%
        148 bp
        3.9
        Other_ZTK7FIAN1_1
        5.3%
        62%
        145 bp
        2.3
        Other_ZTK7FIAN1_2
        5.2%
        62%
        145 bp
        2.3
        PXO_OU8NYIPF2_1
        24.1%
        47%
        141 bp
        1.8
        PXO_OU8NYIPF2_2
        23.2%
        47%
        141 bp
        1.8
        RIO_D2MY5IVLQ_1
        10.8%
        51%
        142 bp
        16.9
        RIO_D2MY5IVLQ_2
        10.7%
        51%
        142 bp
        16.9
        RIO_FC5J6GSS6_1
        15.5%
        46%
        143 bp
        26.4
        RIO_FC5J6GSS6_2
        15.5%
        46%
        143 bp
        26.4
        RIO_G3IOWBWLL_1
        9.1%
        55%
        140 bp
        9.1
        RIO_G3IOWBWLL_2
        8.9%
        55%
        140 bp
        9.1
        RIO_IZTK08VAV_1
        7.6%
        54%
        138 bp
        13.4
        RIO_IZTK08VAV_2
        7.5%
        54%
        138 bp
        13.4
        RIO_MF8QH0DP8_1
        8.2%
        54%
        139 bp
        6.0
        RIO_MF8QH0DP8_2
        8.1%
        54%
        139 bp
        6.0
        TAI_VS1RJYEU2_1
        25.7%
        63%
        132 bp
        2.7
        TAI_VS1RJYEU2_2
        25.5%
        63%
        132 bp
        2.7
        TOK_2LEFVYTCU_1
        9.1%
        61%
        136 bp
        3.1
        TOK_2LEFVYTCU_2
        8.9%
        61%
        136 bp
        3.1
        TOK_41BUJN7YJ_1
        14.2%
        47%
        140 bp
        16.1
        TOK_41BUJN7YJ_2
        13.9%
        47%
        140 bp
        16.1
        TOK_8GN68BXFP_1
        23.4%
        63%
        135 bp
        1.5
        TOK_8GN68BXFP_2
        23.2%
        63%
        135 bp
        1.5
        TOK_9W6FPWDH1_1
        10.7%
        46%
        142 bp
        7.2
        TOK_9W6FPWDH1_2
        10.5%
        46%
        142 bp
        7.2
        TOK_D1NOXQL0L_1
        9.6%
        52%
        145 bp
        16.6
        TOK_D1NOXQL0L_2
        9.5%
        52%
        145 bp
        16.6
        TOK_EZO4LULQ4_1
        12.4%
        46%
        145 bp
        15.2
        TOK_EZO4LULQ4_2
        12.2%
        46%
        145 bp
        15.2
        TOK_N2P2DPKIY_1
        15.8%
        49%
        141 bp
        13.6
        TOK_N2P2DPKIY_2
        15.5%
        49%
        141 bp
        13.6
        TOK_SM080U360_1
        10.8%
        40%
        144 bp
        17.5
        TOK_SM080U360_2
        10.6%
        40%
        144 bp
        17.5
        TOK_XV92PXO2D_1
        13.9%
        49%
        142 bp
        19.4
        TOK_XV92PXO2D_2
        13.6%
        49%
        142 bp
        19.4
        Unknown_YSOUSNDN9_1
        8.3%
        64%
        138 bp
        2.8
        Unknown_YSOUSNDN9_2
        8.1%
        64%
        138 bp
        2.8

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

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        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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